Reproducible workflows
2024-02-19
RStudio (Projects & Setting/preferences)
Generate reports from code (Quarto Scientific Publishing system)
You should have the latest version of Quarto!!
R for Lunch: a lunchtime learning series
See Also: Online Resources: (Rfun | CDVS resources)
Data Management (Plans, Reproducibility, Repositories)
Data Science
Data Visualization
GIS and Spatial Analysis
Data Sources
Code in RStudio
Report types: A select list of Quarto output formats
Use Git and GitHub for version control, code sharing, and collaboration
New Project > Quarto Project
Do use code notebooks
Do use relative file paths and {here}
Do use Restart R and Run All Chunks
Do not rewrite code for different computers
Do not use setwd()
Do not use rm(list=ls())
Global options > Code ^^<- Global options > GeneralUse a bibliography manager such as Zotero
Then,
RStudio > Quarto Notebook > Insert > Citation
Example DOI: 10.18637/jss.v059.i10
Full Instructions
Steps (simplified)
In CLI (terminal, powershell, bash, etc.): quarto publish (For select Quarto project types)
Choose a destination (e.g. quarto.pub or netlify.com)
quarto create > project > manuscript
usethis::use_git()_quarto.yml: change jats: default to pdf: default
Create reproducible environments for your R projects by storing the exact versions of the code interpreter and r packages within the version-control repo
renv::init()renv::snapshot()renv::restore()
The Binder project makes it easy to share live compute environments. This is documented very well at Quarto.
In essence:
quarto use binderaskData@duke.edu
https://library.duke.edu/data
https://is.gd/littleconsult